|
| 1 | +- [Introduction](#introduction) |
| 2 | +- [The contribution process](#the-contribution-process) |
| 3 | + - [Raise an issue](#raise-an-issue) |
| 4 | + - [Create a fork](#create-a-fork) |
| 5 | + - [Create a new folder](#create-a-new-folder) |
| 6 | + - [Add license](#add-license) |
| 7 | + - [Create a notebook](#create-a-notebook) |
| 8 | + - [Commit new changes](#commit-new-changes) |
| 9 | + - [Open a pull request](#open-a-pull-request) |
| 10 | + - [Common recommendations for the review](#common-recommendations-for-the-review) |
| 11 | +- [CI/CD test passing guide](#cicd-test-passing-guide) |
| 12 | + - [PEP 8 Style](#pep-8-style) |
| 13 | + - [Notebook execution](#notebook-execution) |
| 14 | + - [Format requirements](#format-requirements) |
| 15 | +- [Benchmarking result report](#benchmarking-result-report) |
| 16 | + |
| 17 | +## Introduction |
| 18 | + |
| 19 | +Thank you for considering a contribution to the MONAI Tutorials Repository and reading the Contributing Guidelines. |
| 20 | + |
| 21 | +The following is a set of guidelines for contributing tutorials to Project MONAI. |
| 22 | +We want the guidelines to support the growth of the project, instead of restricting the depth and breadth of your contribution. |
| 23 | +If you have any questions about the guideline, please communicate with us and we are happy to discuss them with you. |
| 24 | +MONAI is an open-source project and its success relies on the entire community. |
| 25 | + |
| 26 | +Please feel free to propose changes to this document in a pull request (PR). |
| 27 | + |
| 28 | +## The contribution process |
| 29 | + |
| 30 | +### Raise an issue |
| 31 | + |
| 32 | +We encourage you to [raise an issue](https://github.com/Project-MONAI/tutorials/issues/new/choose) about your needs for MONAI tutorials. |
| 33 | +Conversations help better define the feature and allow other contributors in the community to provide feedback. |
| 34 | + |
| 35 | +### Create a fork |
| 36 | + |
| 37 | +When you are ready to kick off some coding, [create a new fork](https://github.com/Project-MONAI/tutorials/fork) of the `main` branch of this repository. |
| 38 | + |
| 39 | +After forking is complete, you can `git clone` the forked repo to your development environment, and use `git checkout -b` to create a new branch to freely experiment with your changes. |
| 40 | + |
| 41 | +For example: |
| 42 | +```bash |
| 43 | +git clone https://github.com/<your github space>/tutorials.git |
| 44 | +git checkout -b <your new branch name> |
| 45 | +``` |
| 46 | + |
| 47 | +### Create a new folder |
| 48 | + |
| 49 | +MONAI tutorials covered examples of various medical applications and technical topics. |
| 50 | +Tutorials under the same topic/application share the same folder under the root directory, e.g. `2d_classification`, `2d_segmentation`, `3d_classification`, and `3d_segmentation`. |
| 51 | + |
| 52 | +To hold your work in a new location, you can choose to create a new subfolder under the existing ones, or a folder under the root directory if it doesn't belong to any of the existing topics/applications. |
| 53 | + |
| 54 | +The folder should have a `README.md` file with descriptive information for others to start using your code or tutorial notebooks. |
| 55 | + |
| 56 | +Finally, the MONAI tutorial has a [README file](README.md) to communicate the important information and provide an overview of the tutorials and examples. For new tutorials, please add a new entry to the [List](README.md#4-list-of-notebooks-and-examples) of notebooks and [examples](README.md#4-list-of-notebooks-and-examples). |
| 57 | + |
| 58 | +### Add license |
| 59 | + |
| 60 | +All source code and notebook files should include copyright information at the top of the file. |
| 61 | + |
| 62 | +NOTE: for Jupyter Notebook `.ipynb` files, the copyright information should appear at the top of the first markdown cell. |
| 63 | +There are extra two spaces at the end of each line to ensure no line auto-wrap in the markdown rendering in the display. |
| 64 | + |
| 65 | +```markdown |
| 66 | +Copyright (c) MONAI Consortium |
| 67 | +Licensed under the Apache License, Version 2.0 (the "License"); |
| 68 | +you may not use this file except in compliance with the License. |
| 69 | +You may obtain a copy of the License at |
| 70 | + http://www.apache.org/licenses/LICENSE-2.0 |
| 71 | +Unless required by applicable law or agreed to in writing, software |
| 72 | +distributed under the License is distributed on an "AS IS" BASIS, |
| 73 | +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
| 74 | +See the License for the specific language governing permissions and |
| 75 | +limitations under the License. |
| 76 | + |
| 77 | +``` |
| 78 | + |
| 79 | +### Create a notebook |
| 80 | + |
| 81 | +Jupyter Notebook is the preferred way of writing a new MONAI tutorial because we encourage contributors to visualize the outputs and keep the records with the code. |
| 82 | + |
| 83 | +Writing a notebook is easy and flexible, but we require all tutorial notebooks to start with the following three sections: |
| 84 | + |
| 85 | +- Title of the notebook with [licensing information](#add-license) in one markdown cell |
| 86 | +- A markdown cell with `## Setup environment` and a code cell that executes `pip install` shell commands with the exclamation mark `!` to install all the packages necessary for your tutorial. |
| 87 | + |
| 88 | + For example, we install [MONAI with extra dependencies](https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies) and `matplotlib` to set up the environment for the [mednist_tutorial](./2d_classification/mednist_tutorial.ipynb): |
| 89 | + |
| 90 | + ``` |
| 91 | + !python -c "import monai" || pip install -q "monai-weekly[pillow, tqdm]" |
| 92 | + !python -c "import matplotlib" || pip install -q matplotlib |
| 93 | + ``` |
| 94 | +
|
| 95 | +- A markdown cell with `## Setup imports` and a code cell that contains **ALL** import statements and ends with `monai.config.print_config()`: |
| 96 | +
|
| 97 | + ```python |
| 98 | + import numpy as np |
| 99 | +
|
| 100 | + from monai.config import print_config |
| 101 | + from monai.data import DataLoader |
| 102 | + ... |
| 103 | +
|
| 104 | + print_config() |
| 105 | + ``` |
| 106 | +
|
| 107 | +Following this guideline, we prepare some [templates](.github/contributing_templates/notebook/README.md) for contributors to start with. |
| 108 | +
|
| 109 | +### Commit new changes |
| 110 | +
|
| 111 | +MONAI enforces the [Developer Certificate of Origin](https://developercertificate.org/) (DCO) on all pull requests. |
| 112 | +All commit messages should contain the `Signed-off-by` line with an email address. |
| 113 | +The [GitHub DCO app](https://github.com/apps/dco) is deployed on MONAI. |
| 114 | +The pull request's status will be `failed` if commits do not contain a valid `Signed-off-by` line. |
| 115 | +
|
| 116 | +Git has a `-s` (or `--signoff`) command-line option to append this automatically to your commit message: |
| 117 | +```bash |
| 118 | +git commit -s -m 'your awesome commit summary' |
| 119 | +``` |
| 120 | +The commit message will be: |
| 121 | +``` |
| 122 | + your awesome commit summary |
| 123 | +
|
| 124 | + Signed-off-by: Your Name <yourname@example.org> |
| 125 | +``` |
| 126 | + |
| 127 | +Full text of the DCO: |
| 128 | +``` |
| 129 | +Developer Certificate of Origin |
| 130 | +Version 1.1 |
| 131 | +
|
| 132 | +Copyright (C) 2004, 2006 The Linux Foundation and its contributors. |
| 133 | +1 Letterman Drive |
| 134 | +Suite D4700 |
| 135 | +San Francisco, CA, 94129 |
| 136 | +
|
| 137 | +Everyone is permitted to copy and distribute verbatim copies of this |
| 138 | +license document, but changing it is not allowed. |
| 139 | +
|
| 140 | +
|
| 141 | +Developer's Certificate of Origin 1.1 |
| 142 | +
|
| 143 | +By making a contribution to this project, I certify that: |
| 144 | +
|
| 145 | +(a) The contribution was created in whole or in part by me and I |
| 146 | + have the right to submit it under the open source license |
| 147 | + indicated in the file; or |
| 148 | +
|
| 149 | +(b) The contribution is based upon previous work that, to the best |
| 150 | + of my knowledge, is covered under an appropriate open source |
| 151 | + license and I have the right under that license to submit that |
| 152 | + work with modifications, whether created in whole or in part |
| 153 | + by me, under the same open source license (unless I am |
| 154 | + permitted to submit under a different license), as indicated |
| 155 | + in the file; or |
| 156 | +
|
| 157 | +(c) The contribution was provided directly to me by some other |
| 158 | + person who certified (a), (b) or (c) and I have not modified |
| 159 | + it. |
| 160 | +
|
| 161 | +(d) I understand and agree that this project and the contribution |
| 162 | + are public and that a record of the contribution (including all |
| 163 | + personal information I submit with it, including my sign-off) is |
| 164 | + maintained indefinitely and may be redistributed consistent with |
| 165 | + this project or the open source license(s) involved. |
| 166 | +``` |
| 167 | + |
| 168 | +### Open a pull request |
| 169 | + |
| 170 | +Once the changes are ready, push your local branch to the remote, e.g. `git push --set-upstream origin <your new branch name>`, and [open a pull request](https://github.com/Project-MONAI/tutorials/pulls). |
| 171 | +When the pull request is opened, the MONAI repository has a set of GitHub actions that will run checks on the changes. |
| 172 | + |
| 173 | +Please check more [details in the guidelines](#ci-test-passing-guide) for how to pass the tests. |
| 174 | + |
| 175 | +In addition, the team will perform diligent code reviews following this [set of guidelines](#common-recommendations-for-the-review) to reduce the amount of work for users to run the tutorials. |
| 176 | + |
| 177 | +### Common recommendations for the review |
| 178 | + |
| 179 | +Here are some recommendations to make your pull requests faster to review: |
| 180 | +- Note dataset availability. The contributor needs to provide info on how to access the dataset and make a note about the dataset's licensing info. For example, some datasets may be used for non-commercial purposes only. If the dataset can be directly downloaded from a public source on the internet, please consider using the folder specified by `MONAI_DATA_DIRECTORY` to store the dataset files as the [example notebook](.github/contributing_templates/notebook/example_feature.ipynb) shows. |
| 181 | + |
| 182 | +- Avoid large files. Dataset files should be removed from the PR contribution. The overall size of the notebook should be kept down to a few megabytes. |
| 183 | +- Clean up long text outputs generated by Jupyter notebook code cells. |
| 184 | +- Remove private information from the notebook. For example, the user name in the file paths in the notebook outputs and metadata. |
| 185 | +- Be aware of the Hyperlink usage in the notebook: |
| 186 | + - Avoid linking MONAI tutorial resources in the repo using web links (instead, use relative file paths) |
| 187 | + - Avoid linking folders (folder links do not work well in Jupyter notebooks) |
| 188 | + - For graphs, it is recommended to download them and add them to the repo in the `./figure` folder under the root directory |
| 189 | + |
| 190 | +If your tutorial includes network training pipelines, we encourage implementations to scale the training on multiple GPUs. |
| 191 | +For example, if you are using `torchrun` for multi-GPU training, please feel free to include the Python scripts in your tutorial. |
| 192 | + |
| 193 | +## CI/CD test passing guide |
| 194 | + |
| 195 | +The testing system uses `papermill` to run the notebooks. |
| 196 | +To verify the tutorial notebook locally, you can `pip install jupytext flake8 papermill` and then issue the following command with the full path to the notebook file. |
| 197 | + |
| 198 | +``` |
| 199 | +./runner.sh -t <path to your .ipynb file> |
| 200 | +``` |
| 201 | + |
| 202 | +NOTE: the argument after `-t` provides a filename for the `runner.sh` to locate a single notebook in the tutorial to run tests on. |
| 203 | +It is equivalent to using a regex pattern in the argument `-p` or `--pattern` to search for files to run checks. |
| 204 | +In this case, we can also use `-wholename` to specify the only notebook file we would like to check. |
| 205 | +The path must begin with `./`, for example: |
| 206 | +``` |
| 207 | +./runner.sh -p "-and -wholename './2d_classification/mednist_tutorial.ipynb'" |
| 208 | +``` |
| 209 | + |
| 210 | +If you have multiple notebooks to test, please consider designing a regex pattern to locate all the notebook files and use `-p`. |
| 211 | + |
| 212 | +The `runner.sh` includes three kinds of checks: PEP 8 Style, notebook execution, and format requirement. |
| 213 | + |
| 214 | +### PEP 8 Style |
| 215 | + |
| 216 | +PEP 8 is a set of guidelines for writing Python code. |
| 217 | +It was created to improve the readability and consistency of Python code, and to make it easier for people to understand and maintain. |
| 218 | + |
| 219 | +The guidelines cover a wide range of topics, including naming conventions, indentation, white space, and comments. |
| 220 | +They also include recommendations for how to structure and format your code, as well as how to write comments and documentation. |
| 221 | + |
| 222 | +PEP8 style is required for all Python code in `.py` script files and the cell blocks in Jupyter notebooks for the MONAI tutorial. |
| 223 | +Here is a set of common mistakes that lead to check failures: |
| 224 | +- A blank line at end of the cell |
| 225 | +- Extra blank spaces at the end of some lines |
| 226 | +- Module import is not in the `Setup import` cell |
| 227 | +- Import an unused module or create an unused variable |
| 228 | +It needs to note that `--autofix` needs a few additional packages to help you fix some of the issues automatically, and most others need your manual correction. |
| 229 | + |
| 230 | +To run the PEP 8 tests locally, you can use this argument `--no-run` to run the scan only: |
| 231 | + |
| 232 | +``` |
| 233 | +./runner.sh -t <path to your .ipynb file> --no-run |
| 234 | +``` |
| 235 | + |
| 236 | +### Notebook execution |
| 237 | + |
| 238 | +The CI/CD in the pull request process does not execute a Jupyter notebook. |
| 239 | +But the MONAI tutorial has scheduled scans to check if all notebooks can be executed regularly. |
| 240 | + |
| 241 | +The notebook must be in a self-contained state, e.g. setting up the Python environment, downloading the dataset, performing the analysis, and preferably, cleaning up the intermediate files generated from the execution. |
| 242 | + |
| 243 | +During integration testing, we run these notebooks. |
| 244 | +To save time, we modify variables to avoid unnecessary `for` loop iterations. |
| 245 | +For example, the testing system will search for `max_epoch` in the notebook, and set to value to `1` for faster notebook testing. |
| 246 | + |
| 247 | +Hence, during training please use the variables: |
| 248 | +- `max_epochs` for the number of training epochs |
| 249 | +- `val_interval` for the validation interval |
| 250 | + |
| 251 | +On the other hand, if the training is not part of your tutorial, or doesn't use the idea of epochs, please update the exclusion list of `doesnt_contain_max_epochs` in the [runner.sh](runner.sh). |
| 252 | +This lets the runner know that it's not a problem if it doesn't find `max_epochs`. |
| 253 | + |
| 254 | +If you have any other variables that would benefit from setting them to `1` during testing, add them to `strings_to_replace` in `runner.sh`. |
| 255 | +These variables have been added to the list by other contributors: |
| 256 | +- `disc_train_interval` for GAN discriminator training inteval |
| 257 | +- `disc_train_steps` for GAN discriminator training steps |
| 258 | +- `num_batches_for_histogram` |
| 259 | + |
| 260 | +Finally, if your tutorial is not suitable for automated testing, please exclude the notebook by updating the `skip_run_papermill` in the [runner.sh](runner.sh). |
| 261 | +You can append another line in the `skip_run_papermill`: |
| 262 | +``` |
| 263 | +skip_run_papermill=("${skip_run_papermill[@]}" .*<name of your notebook>*) |
| 264 | +``` |
| 265 | + |
| 266 | +If `runner.sh` is modified in your PR, the file permission of `runner.sh` could be set incorrectly in some cases. |
| 267 | +Please ensure the file permission is set to `-rwxrwxr-x` so that our test system can load the script. |
| 268 | +For more information about how to change file permission in git version control, this [StackOverflow page](https://stackoverflow.com/questions/10516201/updating-and-committing-only-a-files-permissions-using-git-version-control) could be helpful. |
| 269 | + |
| 270 | +### Format requirements |
| 271 | + |
| 272 | +The CI/CD will check the following formats, in addition to PEP 8: |
| 273 | +- [Licensing information](#add-license) |
| 274 | +- [Environment and imports](#create-a-notebook) |
| 275 | +- [Output text length](#common-recommendations-for-the-review) |
| 276 | + |
| 277 | +## Benchmarking result report |
| 278 | + |
| 279 | +To standardize all result reporting, the MONAI team recommends contributors use A100 as the standard device for benchmarking in all notebooks. |
| 280 | +If contributors have difficulties getting the computation resources, please contact our team for support. |
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